This function stores add an item named flagScheme
to the metadata
slot of an object inheriting from
'>oce. This is a list containing two
items: name
and mapping
, as provided in the
function arguments.
The purpose is both to document a flag scheme
and to make it so that initializeFlags()
,
setFlags()
and handleFlags()
can specify flags by
name, as opposed to number. This is a generic function,
that may be specialized to the class of object
(see “Details”).
# S4 method for oce
initializeFlagScheme(
object,
name = NULL,
mapping = NULL,
default = NULL,
debug = 0
)
An oce object.
Character value naming the scheme. If this refers
to a pre-defined scheme, then mapping
must not be provided.
A list of named items describing the mapping from
flag meaning to flag numerical value, e.g list(good=1, bad=2)
might be used for a hypothetical class.
Integer vector of flag values that are not considered
to be good. If this is not provided, but if name
is "argo"
,
"BODC"
,
"DFO"
,
"WHP bottle"
, or
"WHP CTD"
, then a conservative value will be set automatically,
equal to the list of flag values that designate bad or questionable data.
For example, for name="WHP CTD"
, the setting will be
c(1,3,4,5,6,7,9)
, leaving only value 2
, which corresponds
with "acceptable" in the notation used for that flag scheme.
Integer set to 0 for quiet action or to 1 for some debugging.
An object with the metadata
slot containing flagScheme
.
This function was added in early May, 2018, and is likely to undergo changes until the autumn of that year. Use with caution.
The following pre-defined schemes are available (note that the names are simplified from the phrases used in defining documentation):
name="argo"
defaults mapping
to
list(not_assessed=0, passed_all_tests=1, probably_good=2, probably_bad=3, bad=4, averaged=7, interpolated=8, missing=9)
See reference 1 for a deeper explanation of the meanings of these codes.
name="BODC"
defaults mapping
to
list(no_quality_control=0, good=1, probably_good=2, probably_bad=3, bad=4, changed=5, below_detection=6, in_excess=7, interpolated=8, missing=9)
See reference 2 for a deeper explanation of the meanings of these codes,
and note that codes A
and Q
are not provided in
oce.
name="DFO"
defaults mapping
to
list(no_quality_control=0, appears_correct=1, appears_inconsistent=2, doubtful=3, erroneous=4, changed=5, qc_by_originator=8, missing=9)
See reference 3 for a deeper explanation of the meanings of these codes.
name="WHP bottle"
defaults mapping
to
list(no_information=1, no_problems_noted=2, leaking=3, did_not_trip=4, not_reported=5, discrepency=6, unknown_problem=7, did_not_trip=8, no_sample=9)
See reference 4 for a deeper explanation of the meanings of these codes.
name="WHP CTD"
defaults mapping
to
list(not_calibrated=1, acceptable=2, questionable=3, bad=4, not_reported=5, interpolated=6, despiked=7, missing=9)
See reference 4 for a deeper explanation of the meanings of these codes.
The codes for "Argo"
are defined at
http://www.oceannetworks.ca/data-tools/data-quality
The codes for "BODC"
are defined at
http://seadatanet.maris2.nl/v_bodc_vocab_v2/browse.asp?order=conceptid&formname=search&screen=0&lib=l20
The codes for "DFO"
are defined at
http://www.dfo-mpo.gc.ca/science/data-donnees/code/list/014-eng.html
The codes for "WHP CTD"
and "WHP bottle"
are defined at
https://www.nodc.noaa.gov/woce/woce_v3/wocedata_1/whp/exchange/exchange_format_desc.htm
Other functions relating to data-quality flags:
defaultFlags()
,
handleFlags,adp-method
,
handleFlags,argo-method
,
handleFlags,ctd-method
,
handleFlags,oce-method
,
handleFlags,section-method
,
handleFlags()
,
initializeFlagScheme,ctd-method
,
initializeFlagScheme,section-method
,
initializeFlagSchemeInternal()
,
initializeFlagScheme()
,
initializeFlags,adp-method
,
initializeFlags,oce-method
,
initializeFlagsInternal()
,
initializeFlags()
,
setFlags,adp-method
,
setFlags,ctd-method
,
setFlags,oce-method
,
setFlags()
Other things related to oce data:
initializeFlagSchemeInternal()
,
initializeFlagScheme()